Enterocytozoon bieneusi is characterized as a ubiquitous intestinal parasite with a wide genetic diversity, and it is capable of infecting a diverse range of hosts all around the world. Since information about the genotype diversity of E. bieneusi in pigs, calves, sheep and goats in Slovakia is very limited, we examined three farms where we mapped the occurrence of E. bieneusi and its genotypes, thus contributing to the information about geographic diversity of this pathogen worldwide. In this study we used PCR methods to examine 253 fecal samples from pigs, calves, sheep and goats with suspected microsporidiosis. Real time PCR was used to identify genotypes by amplification of SSU region and ITS region. After analysis we detected presence of E. bieneusi (7) and Microsporidia sp. (6) in 13 samples. The analysis of nucleotide sequences of ITS region of E. bieneusi shows, that the positive isolates belonged to 5 genotypes, including two known genotypes (I, F) and three new genotypes diagnosed in pigs, named SVK-S1, SVK-S2 and SVK-S3. Phylogenetic analysis showed that these novel genotypes identified in present study belong to group 1, which previously has been described as a zoonotic group. Genotype I was detected in two calves and genotype F was detected in two pigs.
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